CSI-ANN: Discover functional DNA elements based on their epigenetic profiles

miPALM: Infer gene modules from molecular interaction networks

CoSBI: Identify combinatorial chromatin modification patterns across genomic loci

MAPIT: Identify deregulated molecular pathways by integrating expression, DNA methylation, and protein-protein interaction data

SS-CoSBI: Identify combinatorial chromatin modification patterns by semi-supervised biclustering

FCOP: Identify context-specific combinatorial interactions among transcription factors using ChIP-Seq data

IM-PET: Identify target promoters of distal transcriptional enhancers by integrating multiple types of genomics data

M-Module: Simultaneous analysis of multiple functional gene networks to identify shared and network-specific modules

4DGenome: a comprehensive database of chromatin interactions